To explore the gut microbiome composition and community structure, we collected 4 amphipod species sampled from four sampling sites were collected including Mariana Trench, Marceau Trench, the East of New Britain Trench and the Center of New Briton Trench. The gut microbiome communities of the amphipods were analyzed by 16S rRNA-RFLP (restriction fragment length polymorphism) method to compare the gut microbial community between the different sampling sites. The diversity index and rarefaction curves showed significant differences among these four sampling sites. For Hirondellea gigas sampled from Mariana Trench, Psychromonas sp. and uncultured bacterium were the dominant bacterial communities with the ratio of 37.05% and 18.52%, respectively. For the Scopelocheirus schellenbergi sampled from Marceau Trench, Uncultured Mollicutes bacterium and Uncultured deep-sea bacterium were the dominant communities with the ratio of 62.50% and 25.0%, respectively. For Alicella gigantean sampled from the East of New Britain Trench, the dominant communities were Uncultured Mollicutes bacterium (50.0%) and Uncultured Mycoplasmataceae bacterium (44.44%). As for the A. gigantean sampled from the Center of New Britain Trench, the dominant communities were Psychromonas sp. (39.29%), Uncultured Mollicutes bacterium (32.14%), Uncultured Mycoplasmataceae bacterium (14.29%) and Uncultured bacterium (10.71%). Uncultured Mollicutes bacterium possess different ratios among four sampling sites, 62.50% for S. schellenbergi from Marceau Trench, 50% for A. gigantean from the Center of New Britain Trench, 32.14% for A. gigantean from the East of New Britain Trench, and 3.70% for H. gigas from Mariana Trench. There existed great differences between the the gut microbiome composition of the hadal amphipods sampled from four sites. H. gigas sampled from Mariana Trench possessed the highest diversity and complexity, followed by S. schellenbergi from Marceau Trench, and A. gigantean from the New Britain Trench was the least.